The Rapid-Screen cDNA Library Panels were designed for full-length gene cloning and require just three sets of PCRs to identify the desired cDNA clone. The first PCR analysis is performed in a 96-well "Master Plate," where each well contains plasmid DNA from 5,000 clones. Having identified the positive well(s) by gel electrophoresis of the reaction products, the second PCR analysis is carried out in the corresponding 96-well "Sub-Plate(s)," which contains all 5,000 clones from the positive well of the Master Plate arrayed at only 50 clones per well. Since this plate contains glycerol stocks of E. coli instead of plasmid DNA, the cells can be diluted and plated out once a positive well(s) has been identified. Analysis of 96 single colonies by PCR leads to the identification of the positive clone from the Sub-Plate well.
To ensure that a clone detected in a specific well in the Master Plate will be represented in the appropriate Sub-Plate, the Sub- Plates were not derived by dilution of individual wells from the Master Plate (a process which may lose specific clones). Instead, the Sub-Plates were generated first and the wells from each Sub-Plate were then pooled to generate the Master Plate. To guarantee that clones from different wells in the Master Plate were each independently-derived, the Sub-Plates were generated with primary transformants that had not been amplified.

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